X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=809c6eb69b427f8466cb97d60322e7a27b6d53ed;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=848d08a30e29c665f028a31c9f9dd97e0a113c5d;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 848d08a..809c6eb 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -18,16 +18,25 @@ class FilterSeqsCommand : public Command {
 
 public:
 	FilterSeqsCommand(string);
+	FilterSeqsCommand();
 	~FilterSeqsCommand() {};
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "filter.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	struct linePair {
-		int start;
-		int num;
-		linePair(long int i, long int j) : start(i), num(j) {}
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
+
 	vector<linePair*> lines;
 	vector<int> processIDS;
 
@@ -49,11 +58,9 @@ private:
 	int driverRunFilter(string, string, string, linePair*);
 	int driverCreateFilter(Filters& F, string filename, linePair* line);
 	#ifdef USE_MPI
-	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<long>&);
-	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);	
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long int>&);	
 	#endif
-	int setLines(string);
-	
 	
 };